2023-04-14-1610

myaseen208 · Apr 14, 2023 · fadce1f · fadce1f
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diff --git a/R/Exam4.3.1.R b/R/Exam4.3.1.R
@@ -24,17 +24,16 @@
 #'
 #' @examples
 #'
-#' data(DataExam4.3.1)
+#' data(DataExam4.3)
 #' library(tidyverse)
 #' library(ggplot2)
 #'
-#' # Pg. 51
-#'
+#' # Pg. 57
 #' fm4.4    <-
 #'   aov(
-#'       formula     = Percent ~ Replication + Pretreatment*SeedLot
-#'     , data        = DataExam4.3.1 %>%
-#'                     filter(Pretreatment != "Control")
+#'       formula     = Percent ~ Repl + Treat*SeedLot
+#'     , data        = DataExam4.3 %>%
+#'                     filter(Treat != "control")
 #'   # , subset
 #'   # , weights
 #'   # , na.action
@@ -48,19 +47,16 @@
 #'    )
 #'
 #'
-#'  # Pg. 54
+#'  # Pg. 57
 #'  anova(fm4.4)
-#'
-#'  library(supernova)
-#'
-#'  supernova(fm4.4)
+#'  model.tables(x = fm4.4, type = "means")
 #'
 #'   library(emmeans)
 #'
 #'
 #'   emmeans(
 #'       object     = fm4.4
-#'     , specs      = ~ Pretreatment
+#'     , specs      = ~ Treat
 #'     , by         = NULL
 #'     , fac.reduce = function(coefs) apply(coefs, 2, mean)
 #'     , contr      =
@@ -72,7 +68,7 @@
 #'
 #'  emmip(
 #'      object        = fm4.4
-#'    , formula       = ~ Pretreatment
+#'    , formula       = ~ Treat
 #'    , type          = c("link", "response", "predict.type")[1]
 #'    , CIs           = c(TRUE, FALSE)[1]
 #'    , PIs           = c(TRUE, FALSE)[2]
@@ -110,7 +106,7 @@
 #'
 #'   emmeans(
 #'         object     = fm4.4
-#'       , specs      = ~ Pretreatment * SeedLot
+#'       , specs      = ~ Treat * SeedLot
 #'       , by         = NULL
 #'       , fac.reduce = function(coefs) apply(coefs, 2, mean)
 #'       , contr      =
@@ -122,7 +118,7 @@
 #'
 #'  emmip(
 #'      object        = fm4.4
-#'    , formula       = SeedLot ~ Pretreatment
+#'    , formula       = SeedLot ~ Treat
 #'    , type          = c("link", "response", "predict.type")[1]
 #'    , CIs           = c(TRUE, FALSE)[1]
 #'    , PIs           = c(TRUE, FALSE)[2]
@@ -136,7 +132,7 @@
 #'
 #'  emmip(
 #'      object        = fm4.4
-#'    , formula       = Pretreatment ~ SeedLot
+#'    , formula       = Treat ~ SeedLot
 #'    , type          = c("link", "response", "predict.type")[1]
 #'    , CIs           = c(TRUE, FALSE)[1]
 #'    , PIs           = c(TRUE, FALSE)[2]

diff --git a/R/Exam4.3.R b/R/Exam4.3.R
@@ -27,14 +27,21 @@
 #' library(tidyverse)
 #' library(ggplot2)
 #'
-#'
-#'  # Pg.
-#'
+#' DataExam4.3 <-
+#'  DataExam4.3 %>%
+#'  mutate(
+#'   Row         = as_factor(Row)
+#' , Column      = as_factor(Column)
+#' , Replication = as_factor(Replication)
+#' , SeedLot     = as_factor(SeedLot)
+#'  )
+#'
+#'  # Pg. 50
 #'  fm4.2    <-
 #'    aov(
-#'        formula     = Percent ~ Replication + Contcomp + SeedLot +
-#'                                Pretreatment/Contcomp + Contcomp /SeedLot +
-#'                                Pretreatment/ Contcomp/SeedLot
+#'        formula     = Percent ~ Repl + Contcomp + SeedLot +
+#'                                Treat/Contcomp + Contcomp /SeedLot +
+#'                                Treat/ Contcomp/SeedLot
 #'       , data      = DataExam4.3
 #'     # , subset
 #'     # , weights
@@ -47,15 +54,15 @@
 #'       , singular.ok = TRUE
 #'       , contrasts   = NULL
 #'      )
+#'
+#'  # Pg. 54
 #'  anova(fm4.2)
 #'
-#'  library(supernova)
 #'
-#'  supernova(fm4.2)
+#'  # Pg. 50
+#'  model.tables(x = fm4.2, type = "means")
 #'
 #'  library(emmeans)
-#'
-#'
 #'    emmeans(
 #'        object     = fm4.2
 #'      , specs      = ~ Contcomp
@@ -84,7 +91,7 @@
 #'
 #'     emmeans(
 #'        object     = fm4.2
-#'      , specs      = ~ Contcomp + Pretreatment
+#'      , specs      = ~ Contcomp + Treat
 #'      , by         = NULL
 #'      , fac.reduce = function(coefs) apply(coefs, 2, mean)
 #'      , contr      =
@@ -96,7 +103,7 @@
 #'
 #'   emmip(
 #'       object        = fm4.2
-#'     , formula       = Contcomp ~ Pretreatment
+#'     , formula       = Contcomp ~ Treat
 #'     , type          = c("link", "response", "predict.type")[1]
 #'     , CIs           = c(TRUE, FALSE)[1]
 #'     , PIs           = c(TRUE, FALSE)[2]
@@ -158,7 +165,7 @@
 #'     theme_classic()
 #'
 #'  DataExam4.3 %>%
-#'    dplyr::group_by(Pretreatment,Contcomp,SeedLot) %>%
+#'    dplyr::group_by(Treat, Contcomp, SeedLot) %>%
 #'    dplyr::summarize(Mean=mean(Percent))
 #'    RESFIT <- data.frame(residualvalue=residuals(fm4.2),fittedvalue=fitted.values(fm4.2))
 #'    ggplot(mapping = aes(x = fitted.values(fm4.2), y = residuals(fm4.2)))+

diff --git a/R/Exam4.4.R b/R/Exam4.4.R
@@ -32,7 +32,9 @@
 #' library(ggplot2)
 #' library(dae)
 #'
-#' fm4.6    <- aov(
+#' # Pg. 58
+#' fm4.6    <-
+#'   aov(
 #'       formula     = Height ~ Rep + Irrig*Ferti*SeedDLot +
 #'                              Error(Rep/Irrig:Ferti)
 #'     , data        = DataExam4.4
@@ -47,13 +49,14 @@
 #'     , singular.ok = TRUE
 #'     , contrasts   = NULL
 #'     )
-#'  summary(fm4.6)
-#'
-#'    library(supernova)
 #'
-#'    supernova(fm4.6)
+#' # Pg. 61
+#'  summary(fm4.6)
 #'
+#' # Pg. 61
+#'  model.tables(x = fm4.6, type = "means")
 #'
+#' # Pg. 61
 #'    emmeans(
 #'        object     = fm4.6
 #'      , specs      = ~ Irrig

diff --git a/data/DataExam4.3.RData b/data/DataExam4.3.RData
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -2,7 +2,7 @@ pandoc: 2.19.2
 pkgdown: 2.0.7
 pkgdown_sha: ~
 articles: {}
-last_built: 2023-04-13T17:37Z
+last_built: 2023-04-14T11:09Z
 urls:
   reference: https://myaseen208.github.io/eda4treeR/reference
   article: https://myaseen208.github.io/eda4treeR/articles

diff --git a/docs/reference/Exam4.3-1.png b/docs/reference/Exam4.3-1.png
diff --git a/docs/reference/Exam4.3-2.png b/docs/reference/Exam4.3-2.png
diff --git a/docs/reference/Exam4.3-3.png b/docs/reference/Exam4.3-3.png
diff --git a/docs/reference/Exam4.3-4.png b/docs/reference/Exam4.3-4.png
diff --git a/docs/reference/Exam4.3-5.png b/docs/reference/Exam4.3-5.png
diff --git a/docs/reference/Exam4.3.1-1.png b/docs/reference/Exam4.3.1-1.png
diff --git a/docs/reference/Exam4.3.1-2.png b/docs/reference/Exam4.3.1-2.png
diff --git a/docs/reference/Exam4.3.1-3.png b/docs/reference/Exam4.3.1-3.png
diff --git a/docs/reference/Exam4.3.1-4.png b/docs/reference/Exam4.3.1-4.png